Dear Gromacs People, I want to calculate free energy differences between two states A and B using g_BAR.
For this I read many papers concerning the overlap between neighboring sample windows (Delta H) but I am still wondering about the following issue: I know, that there has to be an adequate overlap to get accurate free energy differences, but I am not sure, which neighboring sample distributions have to overlap in the gromacs nomenclature. Do the neighboring distributions N(Delta H(lambda=0.05) | lambda=0) AND N(Delta H(lambda=0) | lambda=0.05) have to overlap? Or shall there be an overlap between neighboring distributions calculated from the left side N(Delta H(lambda=0.05) | lambda=0) ; N(Delta H(lambda=0.10) | lambda=0.05) ; N(Delta H(lambda=0.15) | lambda=0.10) ... and then neighboring from the right side N(Delta H(lambda=0) | lambda=0.05) ; N(Delta H(lambda=0.05) | lambda=0.10) ; N(Delta H(lambda=0.10) | lambda=0.15) ... ? I am puzzled, because if one takes a hypothetic stepsize of "1", then one only gets two distributions N(Delta H(lambda=1) | lambda=0) AND N(Delta H(lambda=0) | lambda=1) which then should overlap to get a right free energy difference estimation. Am I right? So, concluding this, the last two cases should be right, but refering to the "mailing-list-question" of Fabian Casteblanco http://gromacs.5086.x6.nabble.com/Free-energy-sampling-using-G-bar-td4455419.html#a4455420 Justin Lemkul replies, that "the histograms look fine [...]. Lots of overlap.", which would result, that all the "left-side" and all the "right-side" neighbor distributions have to overlap, I think Depending on your answer, can you please explain, why thedistributions of your answer have to overlap, and not the others? For this case I calculated the free energy difference with g_BAR of one tripeptide Valine-Leucine-Valine where thepartial charges of the Leucine are turned to "0" from state A to B in steps of "0.02" (see attachement, representative 4 neighboring distributions). In the case, that all the "left side calculated" and all the "right side calculated" neighbor distributions have to overlap, the overlap in the attached file is great, isn't it? But is that really the correct overlap? Thank you in advance, Mike Nemec
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